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aet21 / SCENT

Estimation of Single-Cell Potency with Single Cell Entropy
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How to calculate of SR from sr.o? And the object 'ccat.v' cannot be found. #5

Open Roger-GOAT opened 1 year ago

Roger-GOAT commented 1 year ago

Hi, great package! Thanks for reply my last issue.

In the document, "Because the calculation of SR takes a couple of minutes, we use the precomputed values stored in the vector srChu.v which is part of dataChu. We can now check if SR discriminates hESCs from the multipotent progenitor endothelial cells:" But how to calculate SR from sr.o? The sr.o$SR did not have a barcode.

Another issue: ccat.v <- CompCCAT(exp = lscChu.m, ppiA = net17Jan16.m) Error in CompCCAT(exp = lscChu0.m, ppiA = net17Jan16.m) the object 'ccat.v' cannot be found.

nickhir commented 1 year ago

Hi,

I am not the developer, but I think I might have an idea what causes the ccat.v cannot be found error. I have created a pull request #6 to fix the bug. Essentially the error is caused because your lscChu.m is probably of class dgeMatrix. To fix this you can either install the my SCNET version (devtools::install_github("nickhir/SCENT")) or more simply try to run ccat.v <- CompCCAT(exp = as.matrix(lscChu.m), ppiA = net17Jan16.m)